Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	P	L	Q	H	G	L	I	L	A	A	I	L	F	V	L	G	L	T	G	L	V	I	R	R	N	L	L	F	M	L	I	G	L	E	I	M	I	N	A	S	A	L	A	F	V	V	A	G	S	Y	W	G	Q	T	D	G	Q	V
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100
Sequence		M	Y	I	L	A	I	S	L	A	A	A	E	A	S	I	G	L	A	L	L	L	Q	L	H	R	R	R	Q	N	L	N	I	D	S	V	S	E	M	R	G
Secondary structure
SS confidence
Disorder																																						?	?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 3rko chain K Region: 1 - 100 Aligned: 100 Modelled: 100 Confidence: 100.0% Identity: 100% PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 3rko chain L Region: 5 - 98 Aligned: 91 Modelled: 94 Confidence: 79.7% Identity: 22% PDB header:oxidoreductase Chain: L: PDB Molecule:nadh-quinone oxidoreductase subunit l; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2jo1 chain A Region: 8 - 26 Aligned: 19 Modelled: 19 Confidence: 54.0% Identity: 47% PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles Phyre2 PDB 2jp3 chain A Region: 8 - 26 Aligned: 19 Modelled: 19 Confidence: 49.7% Identity: 21% PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles Phyre2 PDB 3rko chain M Region: 1 - 91 Aligned: 91 Modelled: 91 Confidence: 41.2% Identity: 13% PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2zxe chain G Region: 8 - 26 Aligned: 19 Modelled: 19 Confidence: 40.6% Identity: 42% PDB header:hydrolase/transport protein Chain: G: PDB Molecule:phospholemman-like protein; PDBTitle: crystal structure of the sodium - potassium pump in the e2.2k+.pi2 state Phyre2 PDB 3rko chain N Region: 7 - 91 Aligned: 82 Modelled: 85 Confidence: 25.2% Identity: 22% PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 1ifl chain A Region: 49 - 89 Aligned: 41 Modelled: 41 Confidence: 24.8% Identity: 10% PDB header:virus Chain: A: PDB Molecule:inovirus; PDBTitle: molecular models and structural comparisons of native and2 mutant class i filamentous bacteriophages ff (fd, f1, m13),3 if1 and ike Phyre2 PDB 3kdp chain H Region: 8 - 26 Aligned: 19 Modelled: 19 Confidence: 22.5% Identity: 47% PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 3kdp chain G Region: 8 - 26 Aligned: 19 Modelled: 19 Confidence: 22.5% Identity: 47% PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 1xme chain C domain 1 Region: 7 - 26 Aligned: 20 Modelled: 20 Confidence: 15.8% Identity: 30% Fold: Single transmembrane helix Superfamily: Bacterial ba3 type cytochrome c oxidase subunit IIa Family: Bacterial ba3 type cytochrome c oxidase subunit IIa Phyre2 PDB 3n23 chain E Region: 8 - 24 Aligned: 17 Modelled: 17 Confidence: 11.7% Identity: 41% PDB header:hydrolase Chain: E: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the high affinity complex between ouabain and the2 e2p form of the sodium-potassium pump Phyre2 PDB 3mk7 chain F Region: 62 - 94 Aligned: 33 Modelled: 33 Confidence: 10.4% Identity: 9% PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase Phyre2 PDB 3cto chain E Region: 89 - 100 Aligned: 12 Modelled: 12 Confidence: 10.1% Identity: 33% PDB header:toxin inhibitor Chain: E: PDB Molecule:uncharacterized protein rv3357/mt3465; PDBTitle: crystal structure of m. tuberculosis yefm antitoxin Phyre2 PDB 1v54 chain M Region: 68 - 84 Aligned: 17 Modelled: 17 Confidence: 8.5% Identity: 24% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Family: Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Phyre2 1 c3rkoK_ 2 c3rkoL_ 3 c2jo1A_ 4 c2jp3A_ 5 c3rkoM_ 6 c2zxeG_ 7 c3rkoN_ 8 c1iflA_ 9 c3kdpH_ 10 c3kdpG_ 11 d1xmec1 12 c3n23E_ 13 c3mk7F_ 14 c3ctoE_ 15 d1v54m_

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c3rkoK_ 100.0 100 PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 2 c3rkoL_ 79.7 22 PDB header:oxidoreductase Chain: L: PDB Molecule:nadh-quinone oxidoreductase subunit l; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 3 c2jo1A_ 54.0 47 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 4 c2jp3A_ 49.7 21 PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles 5 c3rkoM_ 41.2 13 PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 6 c2zxeG_ 40.6 42 PDB header:hydrolase/transport protein Chain: G: PDB Molecule:phospholemman-like protein; PDBTitle: crystal structure of the sodium - potassium pump in the e2.2k+.pi2 state 7 c3rkoN_ 25.2 22 PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 8 c1iflA_ 24.8 10 PDB header:virus Chain: A: PDB Molecule:inovirus; PDBTitle: molecular models and structural comparisons of native and2 mutant class i filamentous bacteriophages ff (fd, f1, m13),3 if1 and ike 9 c3kdpH_ 22.5 47 PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 10 c3kdpG_ 22.5 47 PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 11 d1xmec1 15.8 30 Fold:Single transmembrane helix Superfamily:Bacterial ba3 type cytochrome c oxidase subunit IIa Family:Bacterial ba3 type cytochrome c oxidase subunit IIa 12 c3n23E_ 11.7 41 PDB header:hydrolase Chain: E: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the high affinity complex between ouabain and the2 e2p form of the sodium-potassium pump 13 c3mk7F_ 10.4 9 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase 14 c3ctoE_ 10.1 33 PDB header:toxin inhibitor Chain: E: PDB Molecule:uncharacterized protein rv3357/mt3465; PDBTitle: crystal structure of m. tuberculosis yefm antitoxin 15 d1v54m_ 8.5 24 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Family:Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX)

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0